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- PDB-3ka4: Frog M-ferritin with cobalt -

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Basic information

Entry
Database: PDB / ID: 3ka4
TitleFrog M-ferritin with cobalt
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / IRON STORAGE / DIIRON / Iron / Metal-binding
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferritin, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsTosha, T. / Ng, H.L. / Theil, E. / Alber, T. / Bhattasali, O.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Moving Metal Ions through Ferritin-Protein Nanocages from Three-Fold Pores to Catalytic Sites.
Authors: Tosha, T. / Ng, H.L. / Bhattasali, O. / Alber, T. / Theil, E.C.
History
DepositionOct 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,52423
Polymers20,6231
Non-polymers90122
Water4,053225
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)516,578552
Polymers494,95624
Non-polymers21,622528
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area91540 Å2
ΔGint-297 kcal/mol
Surface area132760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.765, 183.765, 183.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-179-

CO

21A-181-

CO

31A-185-

MG

41A-186-

MG

51A-195-

CL

61A-345-

HOH

DetailsBiological unit is a 24-mer generated by F432 symmetry

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Components

#1: Protein Ferritin, middle subunit / Ferritin M / Ferritin H' / Ferritin X


Mass: 20623.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli (E. coli) / References: UniProt: P07798, ferroxidase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2M MgCl2, 0.1M Bicine pH 9.0, 0.1M CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
Details: Mirror 1: plane parabola Pt and Rh-coated Invar steel. Mirror 2: torroid Pt and Rh-coated Si
RadiationMonochromator: KOHZU: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 52653 / Num. obs: 52634 / % possible obs: 100 % / Redundancy: 15 % / Rsym value: 0.089 / Net I/σ(I): 23.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KA3

3ka3


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.93 / SU B: 1.41 / SU ML: 0.025 / SU R Cruickshank DPI: 0.048 / SU Rfree: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2685 5.1 %RANDOM
Rwork0.147 ---
obs0.149 52633 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.5 Å2 / Biso mean: 15.513 Å2 / Biso min: 6.69 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 22 225 1665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211577
X-RAY DIFFRACTIONr_bond_other_d0.0050.021093
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9482146
X-RAY DIFFRACTIONr_angle_other_deg1.69232681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7995204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97124.89494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38515303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1091510
X-RAY DIFFRACTIONr_chiral_restr0.1360.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021806
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02327
X-RAY DIFFRACTIONr_mcbond_it1.9481.5915
X-RAY DIFFRACTIONr_mcbond_other0.811.5367
X-RAY DIFFRACTIONr_mcangle_it2.7421485
X-RAY DIFFRACTIONr_scbond_it4.6413662
X-RAY DIFFRACTIONr_scangle_it6.4614.5645
X-RAY DIFFRACTIONr_rigid_bond_restr2.16832670
X-RAY DIFFRACTIONr_sphericity_free11.7843247
X-RAY DIFFRACTIONr_sphericity_bonded3.89732621
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 195 -
Rwork0.392 3631 -
all-3826 -
obs--99.97 %

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